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Searched refs:indexFileName (Results 1 – 25 of 124) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/bwa/
H A DBwaSparkEngine.java34 private final String indexFileName; field in BwaSparkEngine
48 final String indexFileName, in BwaSparkEngine() argument
54 if (indexFileName != null) { in BwaSparkEngine()
55 this.indexFileName = indexFileName; in BwaSparkEngine()
60 this.indexFileName = IOUtils.getPath(indexFile).getFileName().toString(); in BwaSparkEngine()
101 final String indexFileName = this.indexFileName; in align() local
104 …new ReadAligner(resolveIndexFileName ? SparkFiles.get(indexFileName) : indexFileName, broadcastHea… in align()
121 …ReadAligner( final String indexFileName, final SAMFileHeader readsHeader, final boolean alignsPair… in ReadAligner() argument
122 this.bwaMemIndex = BwaMemIndexCache.getInstance(indexFileName); in ReadAligner()
/dports/textproc/jalingo/jalingo-0.6.0-src/src/ja/lingo/engine/dictionaryindex/builder/
H A DDictionaryIndexBuilder.java35 private String indexFileName; field in DictionaryIndexBuilder
37 public DictionaryIndexBuilder( String indexFileName ) throws IOException { in DictionaryIndexBuilder() argument
38 Arguments.assertNotNull( "indexFileName", indexFileName ); in DictionaryIndexBuilder()
41 this.indexFileName = indexFileName; in DictionaryIndexBuilder()
43 builderFormat = new BuilderFormat( indexFileName ); in DictionaryIndexBuilder()
94 info.setIndexFileName( indexFileName ); in close()
H A DBuilderFormat.java43 public BuilderFormat( String indexFileName ) throws IOException { in BuilderFormat() argument
44 Arguments.assertNotNull( "indexFileName", indexFileName ); in BuilderFormat()
46 this.indexFos = new FileOutputStream( indexFileName ); in BuilderFormat()
/dports/security/rcracki_mt/rcracki_mt_0.7.0_src/rcracki_mt/
H A DRTIReader.cpp41 this->indexFileName = fname + ".index"; in RTIReader()
51 if( stat( indexFileName.c_str(), &indexFileStats ) == -1 ) in RTIReader()
53 std::cerr << "ERROR: stat() for file: " << indexFileName << " FAILED! " << std::endl; in RTIReader()
64 indexFileData = fopen( indexFileName.c_str(), "rb"); in RTIReader()
67 …std::cerr << "ERROR: could not open index file: " << indexFileName.c_str() << " EXITING!" << std::… in RTIReader()
89 this->indexFileName = fname + ".index"; in RTIReader()
99 if( stat( indexFileName.c_str(), &indexFileStats ) == -1 ) in RTIReader()
101 std::cerr << "ERROR: stat() for file: " << indexFileName << " FAILED! " << std::endl; in RTIReader()
112 indexFileData = fopen( indexFileName.c_str(), "rb"); in RTIReader()
115 …std::cerr << "ERROR: could not open index file: " << indexFileName.c_str() << " EXITING!" << std::… in RTIReader()
[all …]
/dports/devel/hadoop2/hadoop-2.7.2-src/hadoop-mapreduce-project/hadoop-mapreduce-client/hadoop-mapreduce-client-core/src/main/java/org/apache/hadoop/mapred/
H A DSpillRecord.java56 public SpillRecord(Path indexFileName, JobConf job) throws IOException { in SpillRecord() argument
57 this(indexFileName, job, null); in SpillRecord()
60 public SpillRecord(Path indexFileName, JobConf job, String expectedIndexOwner) in SpillRecord() argument
62 this(indexFileName, job, new PureJavaCrc32(), expectedIndexOwner); in SpillRecord()
65 public SpillRecord(Path indexFileName, JobConf job, Checksum crc, in SpillRecord() argument
71 SecureIOUtils.openFSDataInputStream(new File(indexFileName.toUri() in SpillRecord()
74 final long length = rfs.getFileStatus(indexFileName).getLen(); in SpillRecord()
85 indexFileName, -1); in SpillRecord()
/dports/textproc/jalingo/jalingo-0.6.0-src/src/ja/lingo/engine/beans/
H A DInfo.java33 private String indexFileName; field in Info
84 return indexFileName; in getIndexFileName()
86 public void setIndexFileName( String indexFileName ) { in setIndexFileName() argument
87 this.indexFileName = indexFileName; in setIndexFileName()
140 ", indexFileName='" + indexFileName + '\'' + in toString()
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie/
H A DBowtieTask.cpp141 if (settings.indexFileName.isEmpty()) { in prepare()
147 settings.indexFileName = settings.refSeqUrl.dirPath() + "/" + indexName; in prepare()
149 …settings.indexFileName = settings.resultFileName.dirPath() + "/" + settings.resultFileName.baseFil… in prepare()
154 QFileInfo file(settings.indexFileName + indexSuffixes[i]); in prepare()
162 QFileInfo file(settings.indexFileName + indexSuffixes[0]); in prepare()
241 arguments.append(settings.indexFileName); in prepare()
377 QString indexFileName = settings.indexFileName; in prepare() local
378 if (indexFileName.isEmpty()) { in prepare()
380 … indexFileName = settings.refSeqUrl.dirPath() + "/" + settings.refSeqUrl.baseFileName(); in prepare()
382 … indexFileName = settings.resultFileName.dirPath() + "/" + settings.resultFileName.baseFileName(); in prepare()
[all …]
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie2/
H A DBowtie2Task.cpp78 if (settings.indexFileName.isEmpty()) { in prepare()
84 settings.indexFileName = settings.refSeqUrl.dirPath() + "/" + indexName; in prepare()
86 …settings.indexFileName = settings.resultFileName.dirPath() + "/" + settings.resultFileName.baseFil… in prepare()
161 arguments.append(settings.indexFileName); in prepare()
263 QString indexFileName = settings.indexFileName; in prepare() local
264 if (indexFileName.isEmpty()) { in prepare()
266 … indexFileName = settings.refSeqUrl.dirPath() + "/" + settings.refSeqUrl.baseFileName(); in prepare()
268 … indexFileName = settings.resultFileName.dirPath() + "/" + settings.resultFileName.baseFileName(); in prepare()
271 … buildIndexTask = new Bowtie2BuildIndexTask(settings.refSeqUrl.getURLString(), indexFileName); in prepare()
/dports/biology/ugene/ugene-40.1/src/plugins/CoreTests/src/
H A DDnaAssemblyTests.cpp62 indexFileName = el.attribute(INDEX_FILE_ATTR); in init()
63 if (!indexFileName.isEmpty()) { in init()
64 indexFileName.prepend(env->getVar("COMMON_DATA_DIR") + "/"); in init()
127 if (indexFileName.isEmpty()) { in prepare()
128 …indexFileName = GUrlUtils::rollFileName(dir + "/" + GUrl(refSeqUrl).baseFileName() + "_index_" + i… in prepare()
137 settings.indexFileName = indexFileName; in prepare()
/dports/devel/hadoop/hadoop-1.2.1/src/mapred/org/apache/hadoop/mapred/
H A DSpillRecord.java52 public SpillRecord(Path indexFileName, JobConf job, String expectedIndexOwner) in SpillRecord() argument
54 this(indexFileName, job, new PureJavaCrc32(), expectedIndexOwner); in SpillRecord()
57 public SpillRecord(Path indexFileName, JobConf job, Checksum crc, in SpillRecord() argument
63 new File(indexFileName.toUri().getPath()), expectedIndexOwner)); in SpillRecord()
65 final long length = rfs.getFileStatus(indexFileName).getLen(); in SpillRecord()
76 indexFileName, -1); in SpillRecord()
/dports/net/liveMedia/live/liveMedia/
H A DMPEG2TransportStreamIndexFile.cpp28 ::MPEG2TransportStreamIndexFile(UsageEnvironment& env, char const* indexFileName) in MPEG2TransportStreamIndexFile() argument
30 fFileName(strDup(indexFileName)), fFid(NULL), fMPEGVersion(0), fCurrentIndexRecordNum(0), in MPEG2TransportStreamIndexFile()
33 u_int64_t indexFileSize = GetFileSize(indexFileName, NULL); in MPEG2TransportStreamIndexFile()
35 env << "Warning: Size of the index file \"" << indexFileName in MPEG2TransportStreamIndexFile()
44 ::createNew(UsageEnvironment& env, char const* indexFileName) { in createNew() argument
45 if (indexFileName == NULL) return NULL; in createNew()
47 = new MPEG2TransportStreamIndexFile(env, indexFileName); in createNew()
/dports/net/liveMedia/live/testProgs/
H A DtestMPEG2TransportStreamTrickPlay.cpp76 char* indexFileName = new char[len+2]; // allow for trailing x\0 in main() local
77 sprintf(indexFileName, "%sx", inputFileName); in main()
79 = MPEG2TransportStreamIndexFile::createNew(*env, indexFileName); in main()
81 *env << "Failed to open index file \"" << indexFileName << "\" (does it exist?)\n"; in main()
/dports/biology/ugene/ugene-40.1/src/plugins/genome_aligner/src/
H A DGenomeAlignerTask.cpp108 if (settings.indexFileName.isEmpty()) { in GenomeAlignerTask()
110 indexFileName = settings.refSeqUrl.dirPath() + "/" + settings.refSeqUrl.baseFileName(); in GenomeAlignerTask()
117 …indexFileName = indexDir + "/" + settings.refSeqUrl.baseFileName() + "." + GenomeAlignerIndex::HEA… in GenomeAlignerTask()
120 indexFileName = settings.indexFileName; in GenomeAlignerTask()
124 taskLog.details(tr("Index file name: %1").arg(indexFileName)); in GenomeAlignerTask()
308 s.indexFileName = indexFileName; in setupCreateIndexTask()
377 return indexFileName; in getIndexPath()
/dports/astro/marble/marble-21.12.3/src/lib/marble/
H A DDiscCache.cpp18 static QString indexFileName( const QString &cacheDirectory ) in indexFileName() function
30 QFile file( indexFileName( m_CacheDirectory ) ); in DiscCache()
49 QFile file( indexFileName( m_CacheDirectory ) ); in ~DiscCache()
76 if ( it.fileName() == indexFileName( m_CacheDirectory ) ) // skip index file in clear()
/dports/games/libretro-scummvm/scummvm-7b1e929/engines/tinsel/
H A Dhandle.cpp102 const char *indexFileName = TinselV1PSX ? PSX_INDEX_FILENAME : INDEX_FILENAME; in SetupHandleTable() local
104 if (f.open(indexFileName)) { in SetupHandleTable()
111 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable()
137 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable()
143 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable()
146 error(CANNOT_FIND_FILE, indexFileName); in SetupHandleTable()
/dports/games/scummvm/scummvm-2.5.1/engines/tinsel/
H A Dhandle.cpp88 const char *indexFileName = TinselV1PSX ? PSX_INDEX_FILENAME : INDEX_FILENAME; in SetupHandleTable() local
90 if (f.open(indexFileName)) { in SetupHandleTable()
97 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable()
123 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable()
129 error(FILE_IS_CORRUPT, indexFileName); in SetupHandleTable()
132 error(CANNOT_FIND_FILE, indexFileName); in SetupHandleTable()
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/Fasta/
H A DFasta.cpp247 string indexFileName = filename + index->indexFileExtension(); in open() local
249 if(stat(indexFileName.c_str(), &stFileInfo) == 0) { in open()
252 stat(indexFileName.c_str(), &index_attrib); in open()
257 index->readIndexFile(indexFileName); in open()
259 cerr << "index file " << indexFileName << " not found, generating..." << endl; in open()
261 index->writeIndexFile(indexFileName); in open()
/dports/databases/kexi/kexi-3.2.0/src/migration/xbase/
H A Dxbasemigrate.cpp343 foreach( const QString& indexFileName, indexFileNames ) { in getConstraints()
352 QString fileExtension = indexFileName.right( 3 ); in getConstraints()
364 if ( index->OpenIndex(qPrintable(indexFileName)) != XB_NO_ERROR ) { in getConstraints()
365 qDebug()<<"Couldn't open index file"<<indexFileName; in getConstraints()
375 qDebug()<<"Expression mismatch in "<<indexFileName; in getConstraints()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/util_sarray/
H A DSArrayIndexSerializer.h35 …static void serialize(const SArrayIndex *index, const QString &indexFileName, const QString &refFi…
36 static void deserialize(SArrayIndex *index, const QString &indexFileName, TaskStateInfo &ti);
H A DSArrayIndexSerializer.cpp31 void SArrayIndexSerializer::serialize(const SArrayIndex *index, const QString &indexFileName, const… in serialize() argument
33 QFile file(indexFileName); in serialize()
34 if (indexFileName.isEmpty() || !file.open(QIODevice::WriteOnly)) { in serialize()
187 void SArrayIndexSerializer::deserialize(SArrayIndex *index, const QString &indexFileName, TaskState… in deserialize() argument
188 QFile file(indexFileName); in deserialize()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/registry/
H A DDnaAssemblyTask.cpp47 settings.indexFileName = settings.refSeqUrl.getURLString(); in setUpIndexBuilding()
53 settings.indexFileName = settings.refSeqUrl.getURLString(); in setUpIndexBuilding()
59 settings.indexFileName = baseUrl; in setUpIndexBuilding()
/dports/biology/mmseqs2/MMseqs2-13-45111/src/commons/
H A DDBWriter.h16 …DBWriter(const char* dataFileName, const char* indexFileName, unsigned int threads, size_t mode, i…
26 char* getIndexFileName() { return indexFileName; } in getIndexFileName()
83 char* indexFileName; variable
/dports/databases/mongodb36/mongodb-src-r3.6.23/src/third_party/timelib-2017.05/zones/
H A Dbuild-idx.php2 $indexFileName = 'timezonedb.idx'; variable
49 file_put_contents( $indexFileName, $idx_data );
/dports/net/liveMedia/live/mediaServer/
H A DDynamicRTSPServer.cpp187 char* indexFileName = new char[indexFileNameLen]; in createNewSMS() local
188 sprintf(indexFileName, "%sx", fileName); in createNewSMS()
190 …ion(MPEG2TransportFileServerMediaSubsession::createNew(env, fileName, indexFileName, reuseSource)); in createNewSMS()
191 delete[] indexFileName; in createNewSMS()
/dports/net/liveMedia/live/liveMedia/include/
H A DMPEG2TransportStreamIndexFile.hh36 char const* indexFileName);
67 MPEG2TransportStreamIndexFile(UsageEnvironment& env, char const* indexFileName);

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